I actually like most of the things Whaley has done, and I wouldn't like losing an above average GM who has made some big mistakes for an unknown. But I think his diminished role will be reporting to a football czar/consultant type along with Rex, if Whaley does stay. He won't be the head honcho in the football ops department IMO.
And the Pegulas can't be fired. However, I reject the notion that the Pegulas automatically know what they're doing running this team. Luckily, you don't get to where they are without self-assessment, and I have the utmost confidence they won't repeat mistakes.